Emma will take a break from the club as she recuperates from her surgery.
She had surgery last week as a result of her battle with the disease.
She said she would need time and patience to return to full health.
At this time, I have to prioritize what I need to do for myself, and I know you will respect that.
The reigning Women's Super League champion will be managed by an assistant manager and general manager will handle media duties.
The club said it would support Emma during her time of need.
A uterus is removed in a surgery which can cause pain in the uterus.
According to the Centers for Disease Control and Prevention, one in 10 women are affected by endometriosis, a condition that can cause pain and heavy periods.
On the day before she won her first WSL title, she had a procedure in the hospital to remove a contraceptive coil which had been inserted to relieve the symptoms of a sickness.
"I can see why women go out of their minds before diagnosis - I can totally relate to that," Hayes told the Telegraph last year.
I don't want it to get on top of me. I don't want it to take over.
A group of people responded to the statement with messages of support for the coach, who has become one of the most respected coaches in football and turned the Blues into a dominant force in the English game.
"We have built a tremendous team over many years and we've adopted a very multi-disciplinary approach so that if situations like this arise, we are capable of responding to the challenge."
The team are very special and we have no doubt they will do everything to maintain their high standards.
You have had to listen to me yelling from the other side of the pitch. I want to hear you even louder because I'll be watching the team on TV while I'm away.
The Blues have won two of their first three games in the WSL.